Consider following scenario : you want to force a BPEL to wait for maximum of 3 (180 seconds) minutes to get reply from a Partner Link. You can set the following timeouts :
a) syncMaxWaitTime to 180;
b) for CubeEngineBean, CubeDeliveryBean and MessageBean to 240 (best is to set it 1-2 minutes more than the syncMaxWaitTime)
c) Global JTA Timeout to 300

As a general rule, you should have following relation between the timeout parameters: